Subject: Re: No Subject Given By The Author

From: Sergey Noskov <[email-masked]>
Date: Sun, 17 Dec 2000 19:45:49 +0800 (CST)

Dear All,

I have a big problems with memory allocation in CHARMM27b1 bothly on SGI
and GNU platfoorms. Unfortunately, I need to make an aproximate normal
mode analysis for medium sized protein ( 5362 atom in all hydrogen force
field). Options like REDU CMP or DIMB diagonalization does not help in
this program. CHARMM error output include a message like :

expanded heap on ***** words
problem with storage
MALLOC set to 0.0

Program can create a reduced basis for normal mode analysis for example IC
FIRST BOND SECOND BOND in order to leave out mode larger than 1000 cm-1
but crushed during the calculation on diagonalization matrix.

Did anybody have the same problem and is it possible to fixed it without
recompilation of CHARMM?

With best regards,

Sergey

Sergey Noskov
Institute of BioMedical Sciences
Academia Sinica 
Taipei 11529,Taiwan R.O.C.
tel:886-2-27899043 (work)
    886-2-26510783 (home)
fax:886-2-27887641
e-mail:[email-masked]

---

From: Rick Venable <[email-masked]>
Date: Sun, 17 Dec 2000 17:23:53 -0500

> expanded heap on ***** words

This indicates that CHARMM asked for some extra memory, which the OS
could not provide.  Since normal modes require a 3N*3N matrix, the
memory needed in Mbytes is

	(8*(3*N)**2)/(1024*1024)	for N=5362	= 1974

or almost 2 Gbytes of memory.  Your system (IRIX or Linux) needs to have
a fairly large amount of physical RAM and more that 2 Gbyte of swap
space configured in order to do this calculation.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]          |    \  /  |=|    position of the FDA; for that,
[email-masked]              \/   |=|    see   http://www.fda.gov  )